Merge pull request #294 from ncats/fixSmartsRender

fixing rendering of CV fragments

gsrs-module-substance-example/pom.xml

@@ -215,7 +215,7 @@
         <dependency>
             <groupId>gov.nih.ncats</groupId>
             <artifactId>molwitch-cdk</artifactId>
-            <version>1.0.12-SNAPSHOT</version>
+            <version>1.0.14-SNAPSHOT</version>
         </dependency>
         <dependency>
             <groupId>org.springframework.boot</groupId>

gsrs-module-substances-api/pom.xml

@@ -32,12 +32,12 @@
         <dependency>
             <groupId>gov.nih.ncats</groupId>
             <artifactId>molwitch</artifactId>
-            <version>0.6.3-SNAPSHOT</version>
+            <version>0.6.5-SNAPSHOT</version>
         </dependency>
         <dependency>
             <groupId>gov.nih.ncats</groupId>
             <artifactId>molwitch-cdk</artifactId>
-            <version>1.0.9</version>
+            <version>1.0.14</version>
         </dependency>
         <dependency>
             <groupId>gov.nih.ncats</groupId>

gsrs-module-substances-core/pom.xml

@@ -46,7 +46,7 @@
         <dependency>
             <groupId>gov.nih.ncats</groupId>
             <artifactId>molwitch-renderer</artifactId>
-            <version>1.0.13-SNAPSHOT</version>
+            <version>1.0.14-SNAPSHOT</version>
         </dependency>
         <dependency>
             <groupId>gov.nih.ncats</groupId>
@@ -214,7 +214,7 @@
         <dependency>
             <groupId>gov.nih.ncats</groupId>
             <artifactId>molwitch</artifactId>
-            <version>0.6.3-SNAPSHOT</version>
+            <version>0.6.5-SNAPSHOT</version>
         </dependency>
 
         <dependency>

gsrs-module-substances-core/src/main/java/gsrs/module/substance/controllers/LegacyGinasAppController.java

@@ -1,6 +1,8 @@
 package gsrs.module.substance.controllers;
 
 import com.fasterxml.jackson.databind.JsonNode;
+
+import gov.nih.ncats.molwitch.Atom;
 import gov.nih.ncats.molwitch.Chemical;
 import gov.nih.ncats.molwitch.MolwitchException;
 import gsrs.cache.GsrsCache;
@@ -296,7 +298,35 @@ private static Chemical parseAndComputeCoordsIfNeeded(String input) throws IOExc
         Chemical c = Chemical.parse(input);
         if(!c.getSource().get().getType().includesCoordinates()){
             try {
+            	// If it's an in-line format, there's an extra cleanup step
+            	// we do to avoid an issue with parsing some query forms
+            	// TODO: this is really a hack because molwitch-cdk considers any
+            	// molecule with a * to be query-based, and turns lots of
+            	// other atoms inside into query atoms. This makes some downstream
+            	// renderer calculations not work well. The solution here is
+            	// to actually parse * atoms as Helium atoms and give them a * alias.
+            	// Since this is only used for rendering, it tends to be okay.
+            	// If this were ever used for "real" calculations we'd need to do
+            	// something more thorough.
+            	String potentialCXSmarts = c.getSource().get().getData();
+
+            	if(potentialCXSmarts.contains("*")) {
+            		//this means there's a query atom
+            		potentialCXSmarts = potentialCXSmarts.replace("[*]", "[He:17]");
+            		potentialCXSmarts = potentialCXSmarts.replace("*", "[He:17]");
+            		c=Chemical.parse(potentialCXSmarts);
+            		c.atoms().filter(at->at.getAtomToAtomMap().isPresent() && at.getAtomToAtomMap().getAsInt()==17)
+            		 .filter(at->"He".equals(at.getSymbol()))
+            		 .forEach(at->{
+            			 Atom aa=at;
+            			 if(!aa.getAlias().isPresent()) {
+            				 aa.setAlias("*");
+            				 aa.setAtomToAtomMap(0);
+            			 }
+            		 });
+            	}
                 c.generateCoordinates();
+
             } catch (MolwitchException e) {
                 throw new IOException("error generating coordinates",e);
             }

gsrs-module-substances-core/src/main/java/gsrs/module/substance/controllers/SubstanceController.java

@@ -1405,7 +1405,6 @@ public byte[] renderChemical (Structure struc, Chemical chem, String format,
                 rendererOptions.changeSettings(newDisplay);
             }
 
-
             //TODO: This would be nice to get back eventually, for standardization:
             //chem.reduceMultiples();
 
@@ -1475,6 +1474,18 @@ public byte[] renderChemical (Structure struc, Chemical chem, String format,
             if (!fullRendererOptions.isShowShadow()) {
                 renderer.setShadowVisible(false);
             }
+//
+//            if (fullRendererOptions.isAddBorder()) {
+//            	renderer.setBorderVisible(true);
+//            	if(fullRendererOptions.getColorBorder()!=null) {
+//            		renderer.setBorderColorARGB(fullRendererOptions.getColorBorder());	
+//            	}            	
+//            }
+//            
+//            if (fullRendererOptions.getColorBg()!=null) {
+//            	renderer.setBorderColorARGB(fullRendererOptions.getColorBg());            	
+//            }
+
 
             ByteArrayOutputStream bos = new ByteArrayOutputStream();
 
@@ -1520,6 +1531,7 @@ private static void preProcessChemical(Chemical c,  RendererOptions renderOption
             boolean hasRgroups=hasRGroups(c);
             int rgroupColor=1;
 
+
             if(hasRgroups){
                 if(fuse){
                     compColor=colorChemicalComponents(c);
@@ -1604,6 +1616,8 @@ public static boolean hasRGroups(Chemical c){
 //			}
 //		}
         boolean r=false;
+
+
         for(Atom ca:c.getAtoms()){
             if(ca.getRGroupIndex().isPresent()){
                 r= true;
@@ -1614,6 +1628,9 @@ public static boolean hasRGroups(Chemical c){
                 if(alias.startsWith("_R")){
                     ca.setRGroup(Integer.parseInt(alias.replace("_R", "")));
                     r= true;
+                }else if(alias.startsWith("R")){
+                    ca.setRGroup(Integer.parseInt(alias.replace("R", "")));
+                    r= true;
                 }
             }
         }

gsrs-module-substances-core/src/main/java/ix/core/chem/InchiStandardizer.java

@@ -55,9 +55,14 @@ public String canonicalSmiles(Structure s, String mol) {
     @Override
     public Chemical standardize(Chemical orig, Supplier<String> molSupplier, Consumer<Value> valueConsumer) throws IOException {
 
-//        if(true){
-//            return orig;
-//        }
+    	// This is currently a no-op for now. The inchi standardizer appears to have some
+    	// bugs that are not well understood.
+    	// In general it's not actually needed, since we tend to use the inchi hasher which will already do a pre-standardization step.
+    	// 
+
+        if(true){
+            return orig;
+        }
         if(orig.getAtomCount() > maxNumberOfAtoms || orig.hasPseudoAtoms()){
             return orig;
         }

gsrs-module-substances-dto/pom.xml

@@ -33,7 +33,7 @@
         <dependency>
             <groupId>gov.nih.ncats</groupId>
             <artifactId>molwitch</artifactId>
-            <version>0.6.3-SNAPSHOT</version>
+            <version>0.6.5-SNAPSHOT</version>
         </dependency>
         <dependency>
             <groupId>gov.nih.ncats</groupId>

gsrs-module-substances-tests/pom.xml

@@ -33,7 +33,7 @@
         <dependency>
             <groupId>gov.nih.ncats</groupId>
             <artifactId>molwitch</artifactId>
-            <version>0.6.3-SNAPSHOT</version>
+            <version>0.6.5-SNAPSHOT</version>
         </dependency>
         <dependency>
             <groupId>gov.nih.ncats</groupId>

installExtraJars.cmd

@@ -1,5 +1,5 @@
 mvnw.cmd install:install-file -Dfile=extraJars/applications-api-3.1-SNAPSHOT.jar
 mvnw.cmd install:install-file -Dfile=extraJars/products-api-3.1-SNAPSHOT.jar
 mvnw.cmd install:install-file -Dfile=extraJars/clinical-trials-api-3.1-SNAPSHOT.jar
-mvnw.cmd install:install-file -Dfile=extraJars/molwitch-renderer-1.0.13-SNAPSHOT.jar
+mvnw.cmd install:install-file -Dfile=extraJars/molwitch-renderer-1.0.14-SNAPSHOT.jar
 

installExtraJars.sh

@@ -1,4 +1,4 @@
 ./mvnw install:install-file -Dfile=extraJars/applications-api-3.1-SNAPSHOT.jar
 ./mvnw install:install-file -Dfile=extraJars/products-api-3.1-SNAPSHOT.jar
 ./mvnw install:install-file -Dfile=extraJars/clinical-trials-api-3.1-SNAPSHOT.jar
-./mvnw install:install-file -Dfile=extraJars/molwitch-renderer-1.0.13-SNAPSHOT.jar
+./mvnw install:install-file -Dfile=extraJars/molwitch-renderer-1.0.14-SNAPSHOT.jar